Figure 1

Example group II intron structure. (A) DNA structure of a group II intron. The intron RNA portion is denoted by red boxes, while conserved ORF domains are in blue. The IEP contains a RT (reverse transcriptase) domain, including conserved sub-domains (0, 1, 2, 2a, 3, 4, 5, 6, 7), an X domain, a D (DNA-binding) domain and an optional En (endonuclease) domain. Intron RNA domains are shown underneath in Roman numerals, and exon 1 and 2 sequences are in black. (B) An example group II intron RNA secondary structure (IIC). The intron sequence is depicted in red lettering, with exon sequences in blue and black. The ORF sequence is represented by the dotted loop in domain IV. IBS1/EBS1 and IBS3/EBS3 (blue and orange shading) represent base pairings between the intron and exons that help to define the intron boundaries during splicing. The sequence shown is for B.h. I1 of Bacillus halodurans.